Mercurial > repos > petr-novak > dante_ltr

annotate tests.sh @ 13:559940c04c44 draft

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"planemo upload commit 139c041f671459192beb10ae45a8b371367c23b6"
author petr-novak
date Thu, 11 Aug 2022 07:29:06 +0000
parents ff01d4263391
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/bin/bash
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2 # set to stop in case of error
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3 set -e
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4 # first argument is cpu number
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5 NCPU_TO_USE=$1
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7 # test if NCPU_TO_USE is set:
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8 if [ -z "${NCPU_TO_USE}" ]; then
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9 echo "NCPU_TO_USE is not set, using 10"
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10 NCPU_TO_USE=10
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11 fi
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13 eval "$(conda shell.bash hook)"
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14 conda activate dante_ltr
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15 echo "Running tests 1, detection of LTRs"
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16 ./detect_putative_ltr.R -s test_data/sample_genome.fasta \
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17 -g test_data/sample_DANTE.gff3 -o tmp/test_output1 -c $NCPU_TO_USE
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20 cat tmp/test_output1_statistics.csv
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21
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22 echo "Running tests 2, filtering gff"
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23 ./clean_ltr.R -g tmp/test_output1.gff3 -s test_data/sample_genome.fasta \
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24 -o tmp/test_output2 -c $NCPU_TO_USE
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25
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26 echo "Running tests 3, detection of LTRs, allow missing domains"
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27 ./detect_putative_ltr.R -s test_data/sample_genome.fasta \
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28 -g test_data/sample_DANTE.gff3 -o tmp/test_output3 -c $NCPU_TO_USE -M 2
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31 cat tmp/test_output3_statistics.csv
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32
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33 echo "Running tests 4, filtering gff"
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34 ./clean_ltr.R -g tmp/test_output3.gff3 -s test_data/sample_genome.fasta \
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35 -o tmp/test_output4 -c $NCPU_TO_USE
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38 echo "Running tests 5, detection of LTRs using python wrapper"
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39 ./detect_putative_ltr_wrapper.py -s test_data/sample_genome.fasta \
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40 -g test_data/sample_DANTE.gff3 -o tmp/test_output5 -c $NCPU_TO_USE \
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41 -S 10000000
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42 cat tmp/test_output5_statistics.csv
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44 echo "Running tests 6, filtering gff"
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45 ./clean_ltr.R -g tmp/test_output5.gff3 -s test_data/sample_genome.fasta \
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46 -o tmp/test_output6 -c $NCPU_TO_USE
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48 /detect_putative_ltr_wrapper.py -s test_data/sample_genome_part.fasta \
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49 -g test_data/sample_DANTE_part.gff3 -o tmp/test_output7 -c $NCPU_TO_USE \
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50 -S 10000000 -M 2